miRNA Mediated Noise Making of 3'UTR Mutations in Cancer

MicroRNA-mediated regulation of nonsense-mediated mRNA decay factors: Insights into microRNA prediction tools and profiling techniques

Nonsense-mediated mRNA decay (NMD) stands out as a prominent RNA surveillance mechanism within eukaryotes, meticulously overseeing both RNA abundance and integrity by eliminating aberrant transcripts. These defective transcripts are discerned through the concerted efforts of translating ribosomes, eukaryotic release factors (eRFs), and trans-acting NMD factors, with Up-Frameshift 3 (UPF3) serving as a noteworthy component. Remarkably, in humans, UPF3 exists in two paralogous forms, UPF3A (UPF3) and UPF3B (UPF3X). Beyond its role in quality control, UPF3 wields significant influence over critical cellular processes, including neural development, synaptic plasticity, and axon guidance. However, the precise regulatory mechanisms governing UPF3 remain elusive. MicroRNAs (miRNAs) emerge as pivotal post-transcriptional gene regulators, exerting substantial impact on diverse pathological and physiological pathways. This comprehensive review encapsulates our current understanding of the intricate regulatory nexus between NMD and miRNAs, with particular emphasis on the essential role played by UPF3B in neurodevelopment. Additionally, we bring out the significance of the 3'-untranslated region (3'-UTR) as the molecular bridge connecting NMD and miRNA-mediated gene regulation. Furthermore, we provide an in-depth exploration of diverse computational tools tailored for the prediction of potential miRNA targets. To complement these computational approaches, we delineate experimental techniques designed to validate predicted miRNA-mRNA interactions, empowering readers with the knowledge necessary to select the most appropriate methodology for their specific research objectives.

Determinants of gastric cancer immune escape identified from non-coding immune-landscape quantitative trait loci

The landscape of non-coding mutations in cancer progression and immune evasion is largely unexplored. Here, we identify transcrptome-wide somatic and germline 3' untranslated region (3'-UTR) variants from 375 gastric cancer patients from The Cancer Genome Atlas. By performing gene expression quantitative trait loci (eQTL) and immune landscape QTL (ilQTL) analysis, we discover 3'-UTR variants with cis effects on expression and immune landscape phenotypes, such as immune cell infiltration and T cell receptor diversity. Using a massively parallel reporter assay, we distinguish between causal and correlative effects of 3'-UTR eQTLs in immune-related genes. Our approach identifies numerous 3'-UTR eQTLs and ilQTLs, providing a unique resource for the identification of immunotherapeutic targets and biomarkers. A prioritized ilQTL variant signature predicts response to immunotherapy better than standard-of-care PD-L1 expression in independent patient cohorts, showcasing the untapped potential of non-coding mutations in cancer.

Identification of Recurrent Mutations in the microRNA-Binding Sites of B-Cell Lymphoma-Associated Genes in Follicular Lymphoma

Follicular lymphoma (FL) is a common indolent B-cell lymphoma that can transform into the more aggressive transformed FL (tFL). However, the molecular process driving this transformation is uncertain. In this work, we aimed to identify microRNA (miRNA)-binding sites recurrently mutated in follicular lymphoma patients, as well as in transformed FL patients. Using whole-genome sequencing data from FL tumors, we discovered 544 mutations located in bioinformatically predicted microRNA-binding sites. We then studied these specific regions using targeted sequencing in a cohort of 55 FL patients, found 16 recurrent mutations, and identified a further 69 variants. After filtering for QC, we identified 21 genes with mutated miRNA-binding sites that were also enriched for B-cell-associated genes by Gene Ontology. Over 40% of mutations identified in these genes were present exclusively in tFL patients. We validated the predicted miRNA-binding sites of five of the genes by luciferase assay and demonstrated that the identified mutations in BCL2 and EZH2 genes impaired the binding efficiency of miR-5008 and miR-144 and regulated the endogenous levels of messenger RNA (mRNA).

FI-Net: Identification of Cancer Driver Genes by Using Functional Impact Prediction Neural Network

Identification of driver genes, whose mutations cause the development of tumors, is crucial for the improvement of cancer research and precision medicine. To overcome the problem that the traditional frequency-based methods cannot detect lowly recurrently mutated driver genes, researchers have focused on the functional impact of gene mutations and proposed the function-based methods. However, most of the function-based methods estimate the distribution of the null model through the non-parametric method, which is sensitive to sample size. Besides, such methods could probably lead to underselection or overselection results. In this study, we proposed a method to identify driver genes by using functional impact prediction neural network (FI-net). An artificial neural network as a parametric model was constructed to estimate the functional impact scores for genes, in which multi-omics features were used as the multivariate inputs. Then the estimation of the background distribution and the identification of driver genes were conducted in each cluster obtained by the hierarchical clustering algorithm. We applied FI-net and other 22 state-of-the-art methods to 31 datasets from The Cancer Genome Atlas project. According to the comprehensive evaluation criterion, FI-net was powerful among various datasets and outperformed the other methods in terms of the overlap fraction with Cancer Gene Census and Network of Cancer Genes database, and the consensus in predictions among methods. Furthermore, the results illustrated that FI-net can identify known and potential novel driver genes.

Regulation of DNA Damage Response and Homologous Recombination Repair by microRNA in Human Cells Exposed to Ionizing Radiation

Ionizing radiation may be of both artificial and natural origin and causes cellular damage in living organisms. Radioactive isotopes have been used significantly in cancer therapy for many years. The formation of DNA double-strand breaks (DSBs) is the most dangerous effect of ionizing radiation on the cellular level. After irradiation, cells activate a DNA damage response, the molecular path that determines the fate of the cell. As an important element of this, homologous recombination repair is a crucial pathway for the error-free repair of DNA lesions. All components of DNA damage response are regulated by specific microRNAs. MicroRNAs are single-stranded short noncoding RNAs of 20–25 nt in length. They are directly involved in the regulation of gene expression by repressing translation or by cleaving target mRNA. In the present review, we analyze the biological mechanisms by which miRNAs regulate cell response to ionizing radiation-induced double-stranded breaks with an emphasis on DNA repair by homologous recombination, and its main component, the RAD51 recombinase. On the other hand, we discuss the ability of DNA damage response proteins to launch particular miRNA expression and modulate the course of this process. A full understanding of cell response processes to radiation-induced DNA damage will allow us to develop new and more effective methods of ionizing radiation therapy for cancers, and may help to develop methods for preventing the harmful effects of ionizing radiation on healthy organisms.

A frequent somatic mutation in the 3'UTR of GAPDH facilitates the development of ovarian cancer by creating a miR‑125b binding site

Ovarian cancer (OVCA) is one of the most common types of cancer in women worldwide. Recent studies have focused on the presence and effect of somatic mutations in patients with OVCA; however, studies on the roles of mutations located in the untranslated regions (UTR) of genes in OVCA remain limited. In the present study, a frequent somatic mutation in the glyceraldehyde 3-phosphate dehydrogenase (GADPH) 3′UTR was identified using transcriptome sequencing of 120 pairs of OVCA tissue samples. The mutant GAPDH 3′UTR promoted tumor growth and cell motility. Furthermore, the mutation in the GAPDH 3′UTR significantly downregulated the levels of mature miR-125b by creating a new miR-125b binding site. Finally, STAT3 levels were increased in SKOV3 cells stably expressing the mutant GADPH 3′UTR, which is a critical target gene of miR-125b. In conclusion, the present study demonstrated that the mutation located in GAPDH 3′UTR promoted OVCA growth and development by sponging miR-125b and thereby affecting STAT3 expression levels.

microRNA-mediated noise processing in cells: A fight or a game?

In the past decades, microRNAs (miRNA) have much attracted the attention of researchers at the interface between life and theoretical sciences for their involvement in post-transcriptional regulation and related diseases. Thanks to the always more sophisticated experimental techniques, the role of miRNAs as "noise processing units" has been further elucidated and two main ways of miRNA noise-control have emerged by combinations of theoretical and experimental studies. While on one side miRNAs were thought to buffer gene expression noise, it has recently been suggested that miRNAs could also increase the cell-to-cell variability of their targets. In this Mini Review, we focus on the role of miRNAs in molecular noise processing and on the advantages as well as current limitations of theoretical modelling.

Up-regulation of microRNA-574 attenuates lipopolysaccharide- or cecal ligation and puncture-induced sepsis associated with acute lung injury

Acute lung injury (ALI) is the most vulnerable organ in sepsis, however, its underlying mechanism remains unclear. Cell viability and apoptosis were detected by cell counting kit-8 and flow cytometry. The expressions of miR-574, Complement 3 (C3), glucose regulatory protein 78 (GRP78), C/EBP homologous protein (CHOP) and Caspase-12 were determined using quantitative real time (qRT)-PCR and Western blot. Histopathology of mice was stained by haematoxylin and eosin staining. The levels of tumour necrosis factor-α (TNF-α) and interleukin (IL)-1β were determined using ELISA. The expression of miR-574 was positively correlated with cell viability in lipopolysaccharide (LPS)-treated cells. Cell viability was improved and apoptosis was inhibited by mimics. Meanwhile, the levels of GRP78, CHOP and Caspase-12 were suppressed by mimics and agomir in LPS-treated human bronchial epithelial (HBE) cells and cecal ligation and puncture (CLP)-treated mice. In vivo, lung tissue damages were ameliorated by agomir, which also decreased the levels of neutrophils, macrophages and albumin. C3 was a target gene of miR-574 and could be decreased by mimics. SiC3 enhanced cell viability and inhibited apoptosis, however, it suppressed the mRNA levels of GRP78, CHOP and Caspase-12. Up-regulation of miR-574 attenuated sepsis-induced lung injury may be by promoting C3 down-regulation and reducing sepsis-induced endoplasmic reticulum stress (ERS). SIGNIFICANCE OF THE STUDY: Clinically, the mortality rate of ALI induced by sepsis remains at a high level, thus, clarifying the mechanism of induction of ALI through pathogen infection will provide a new target for clinical treatment of ALI. In this study, up-regulation of miR-574 attenuated sepsis-induced lung injury may be by promoting C3 down-regulation and reducing sepsis-induced ERS. Our study provides a deeper understanding of sepsis.